Balanced reconstruction codes for single edits

TL;DR

This paper develops asymptotically optimal balanced reconstruction codes for single-edit errors in DNA storage, reducing redundancy and maintaining high code rates compared to unbalanced codes.

Contribution

It introduces the first asymptotically optimal balanced reconstruction codes for single-edit errors, with improved redundancy bounds across all channel variants.

Findings

Redundancy decreases from 1.5 log n to 0.5 log n plus lower order terms.

Balanced codes do not reduce the rate compared to unbalanced codes.

Optimal codes are designed for all fixed numbers of noisy reads.

Abstract

Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is to design codes with sizes as large as possible, such that every codeword can be uniquely reconstructed from any $N$ distinct noisy reads, where $N$ is fixed. In this paper, we study binary reconstruction codes with the constraint that every codeword is balanced, which is a common requirement in the technique of DNA-based storage. For all possible channels with a single edit error and their variants, we design asymptotically optimal balanced reconstruction codes for all $N$, and show that the number of their redundant symbols decreases from $\frac{3}{2}\log_2 n+O(1)$ to $\frac{1}{2}\log_2n+\log_2\log_2n+O(1)$, and finally to $\frac{1}{2}\log_2n+O(1)$ but with different speeds, where $n$ is the length of the code. Compared with the unbalanced case, our results imply that the balanced property does not reduce the rate of the reconstruction code in the corresponding codebook.